ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format

BMC Biotechnology

Correspondence

Elaine T Freund¹  Juli D Klemm²  Stacey L Harper³  David Paik⁴  Dennis G Thomas⁵  Nathan A Baker⁶  Elizabeth Hahn-Dantona⁷  Fred Klaessig⁸  Martin Fritts⁹  Sharon Gaheen⁹  Sue Pan⁹  Grace A Stafford^1,10 

[1] 3rd Millennium, Inc, 02896, North Smithfield, RI, USA;Center for Biomedical Informatics and Information Technology, National Cancer Institute, 20852, Rockville, MD, USA;Department of Environmental and Molecular Toxicology, School of Chemical, Biological and Environmental Engineering, Oregon State University, 97331, Corvallis, OR, USA;Department of Radiology, Stanford University, 94305, Stanford, CA, USA;Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, 99352, Richland, WA, USA;Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, PO Box 999, MSID K7-28, 99352, Richland, WA, USA;Lockheed Martin, 20852, Rockville, MD, USA;Pennsylvania Bio Nano Systems, LLC, Doylestown, PA, USA;SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, 20852, Rockville, MD, USA;The Jackson Laboratory, 04609, Bar Harbor, Maine, USA;

关键词: Material Sample;    File Format;    Material File;    Image File;    Public Repository;   

DOI  :  10.1186/1472-6750-13-2

 received in 2012-04-12, accepted in 2012-12-11,  发布年份 2013

来源: Springer

【 摘 要 】

Background and motivationThe high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials.ResultsWe have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed de novo to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata.ConclusionThe ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption.

【 授权许可】

Unknown   
© Thomas et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.